#setwd('/afs/inf.ed.ac.uk/user/s17/s1725186/Documents/PhD-Models/FirstPUModel/RMarkdowns')

library(tidyverse) ; library(reshape2) ; library(glue) ; library(plotly) ; library(dendextend)
library(RColorBrewer) ; library(viridis) ; require(gridExtra) ; library(GGally)
library(knitr)
library(biomaRt)
library(clusterProfiler) ; library(ReactomePA) ; library(DOSE)

Load preprocessed dataset (preprocessing code in 19_10_14_data_preprocessing.Rmd) and clustering (pipeline in 19_10_21_WGCNA.Rmd)

# Gandal dataset
load('./../Data/preprocessed_data.RData')
datExpr = datExpr %>% data.frame
DE_info = DE_info %>% data.frame


# GO Neuronal annotations: regex 'neuron' in GO functional annotations and label the genes that make a match as neuronal
GO_annotations = read.csv('./../Data/genes_GO_annotations.csv')
GO_neuronal = GO_annotations %>% filter(grepl('neuron', go_term)) %>% 
              mutate('ID'=as.character(ensembl_gene_id)) %>% 
              dplyr::select(-ensembl_gene_id) %>% distinct(ID) %>%
              mutate('Neuronal'=1)


# SFARI Genes
SFARI_genes = read_csv('./../../../SFARI/Data/SFARI_genes_01-03-2020_w_ensembl_IDs.csv')
SFARI_genes = SFARI_genes[!duplicated(SFARI_genes$ID) & !is.na(SFARI_genes$ID),]


# Clusterings
clusterings = read_csv('./../Data/clusters.csv')


# Update DE_info with SFARI and Neuronal information
genes_info = DE_info %>% mutate('ID'=rownames(.)) %>% left_join(SFARI_genes, by='ID') %>% 
  mutate(`gene-score`=ifelse(is.na(`gene-score`), 'None', `gene-score`)) %>%
  left_join(GO_neuronal, by='ID') %>% left_join(clusterings, by='ID') %>%
  mutate(Neuronal=ifelse(is.na(Neuronal), 0, Neuronal)) %>%
  mutate(gene.score=ifelse(`gene-score`=='None' & Neuronal==1, 'Neuronal', `gene-score`), 
         significant=padj<0.05 & !is.na(padj))


clustering_selected = 'DynamicHybrid'
genes_info$Module = genes_info[,clustering_selected]

dataset = read.csv(paste0('./../Data/dataset_', clustering_selected, '.csv'))
dataset$Module = dataset[,clustering_selected]

# Correct SFARI Scores
dataset$gene.score = genes_info$gene.score

# GSEA Results
load('./../Data/GSEA_bonferroni.RData')


SFARI_colour_hue = function(r) {
  pal = c('#FF7631','#FFB100','#E8E328','#8CC83F','#62CCA6','#59B9C9','#b3b3b3','#808080','gray','#d9d9d9')[r]
}

rm(DE_info, GO_annotations, clusterings, getinfo, mart, dds, GO_neuronal)

Module-Diagnosis Correlation

plot_data = dataset %>% dplyr::select(Module, MTcor) %>% distinct

ggplotly(plot_data %>% ggplot(aes(reorder(Module, -MTcor), MTcor)) + geom_bar(stat='identity', fill = plot_data$Module) + theme_minimal() + 
         xlab('Modules')+ ylab('Module-Diagnosis Correlation') + geom_hline(yintercept =c(0.9, -0.9), color = 'gray', linetype = 'dashed') + 
         theme(axis.text.x = element_text(angle = 90, hjust = 1)))

top_modules = plot_data %>% arrange(desc(MTcor)) %>% filter(abs(MTcor)>0.9) %>% dplyr::pull(Module) %>% 
              unique %>% as.character

cat(paste0('Top modules selected: ', paste(top_modules, collapse=', '),'\n'))

## Top modules selected: #73B000, #EE8045, #00B9E3, #84AD00

print_results = function(enrichment_list){
  
  for(module in top_modules){
    
    df = enrichment_list[[module]] %>% dplyr::select(ID, Description, setSize, NES, p.adjust, qvalues) %>% 
         arrange(desc(NES)) %>% filter(NES>0, p.adjust<0.05)
    
    if(nrow(df)>0){
      
      print(kable(df, caption = paste0('Enriched terms for module ', module, ' (MTcor = ', 
                                       round(dataset$MTcor[dataset$Module==module][1],2),')')))
      cat('\n') 
    
    } else {
      df = enrichment_list[[module]] %>% dplyr::select(ID, Description, setSize, NES, p.adjust, qvalues) %>% 
            arrange(desc(NES)) %>% filter(p.adjust<0.05)
      
      if(nrow(df)>0){
        
        print(kable(df, caption = paste0('Negatively Enriched terms for module ', module, ' (MTcor = ', 
                                         round(dataset$MTcor[dataset$Module==module][1],2),')')))
        cat('\n') 
        
      } else cat(paste0('\nNo enrichment found for module ',module,'\n'))
    }
  }
}

GSEA Results

KEGG

print_results(enrichment_KEGG)

Enriched terms for module #73B000 (MTcor = 0.94)
ID	Description	setSize	NES	p.adjust	qvalues
hsa05322	Systemic lupus erythematosus	108	3.153606	0.0059327	0.0002077
hsa05034	Alcoholism	165	2.459042	0.0058904	0.0002077
hsa04061	Viral protein interaction with cytokine and cytokine receptor	52	2.281161	0.0060269	0.0002077
hsa05202	Transcriptional misregulation in cancer	163	2.203888	0.0059057	0.0002077
hsa05144	Malaria	39	2.157958	0.0060429	0.0002077
hsa04392	Hippo signaling pathway - multiple species	26	2.125743	0.0241726	0.0005221
hsa05321	Inflammatory bowel disease (IBD)	47	2.112495	0.0120419	0.0003279
hsa05150	Staphylococcus aureus infection	49	2.105556	0.0060243	0.0002077
hsa04064	NF-kappa B signaling pathway	89	2.084849	0.0059586	0.0002077
hsa04060	Cytokine-cytokine receptor interaction	170	2.038993	0.0058959	0.0002077
hsa05203	Viral carcinogenesis	188	1.947256	0.0058775	0.0002077
hsa05205	Proteoglycans in cancer	190	1.767234	0.0176180	0.0004244
hsa05206	MicroRNAs in cancer	155	1.749387	0.0295820	0.0005615
hsa04510	Focal adhesion	192	1.729820	0.0294080	0.0005615
hsa05168	Herpes simplex virus 1 infection	446	1.684611	0.0056711	0.0002077
hsa05131	Shigellosis	229	1.679445	0.0291453	0.0005615

Enriched terms for module #EE8045 (MTcor = 0.93)
ID	Description	setSize	NES	p.adjust	qvalues
hsa05322	Systemic lupus erythematosus	108	3.116966	0.0051117	0.0002189
hsa05168	Herpes simplex virus 1 infection	446	2.552720	0.0043657	0.0002189
hsa05202	Transcriptional misregulation in cancer	163	2.476862	0.0049160	0.0002189
hsa05150	Staphylococcus aureus infection	49	2.470281	0.0054361	0.0002189
hsa05034	Alcoholism	165	2.468803	0.0049104	0.0002189
hsa04064	NF-kappa B signaling pathway	89	2.297403	0.0052044	0.0002189
hsa04610	Complement and coagulation cascades	61	2.180640	0.0053376	0.0002189
hsa05321	Inflammatory bowel disease (IBD)	47	2.167627	0.0054505	0.0002189
hsa04392	Hippo signaling pathway - multiple species	26	2.114051	0.0394716	0.0007043
hsa04061	Viral protein interaction with cytokine and cytokine receptor	52	2.110892	0.0054038	0.0002189
hsa05320	Autoimmune thyroid disease	28	2.106539	0.0224633	0.0004130
hsa05416	Viral myocarditis	52	2.074541	0.0108075	0.0002249
hsa05134	Legionellosis	52	2.069673	0.0162113	0.0003073
hsa05203	Viral carcinogenesis	188	2.006682	0.0048435	0.0002189
hsa04060	Cytokine-cytokine receptor interaction	170	1.967226	0.0049041	0.0002189
hsa04621	NOD-like receptor signaling pathway	148	1.808400	0.0148797	0.0002912

Enriched terms for module #00B9E3 (MTcor = -0.93)
ID	Description	setSize	NES	p.adjust	qvalues
hsa00190	Oxidative phosphorylation	127	2.755517	0.0047049	0.0001315
hsa05016	Huntington disease	289	2.603602	0.0042150	0.0001315
hsa05012	Parkinson disease	235	2.563026	0.0043358	0.0001315
hsa04723	Retrograde endocannabinoid signaling	142	2.388517	0.0046292	0.0001315
hsa04721	Synaptic vesicle cycle	70	2.379935	0.0050547	0.0001315
hsa05010	Alzheimer disease	348	2.343123	0.0041027	0.0001315
hsa04260	Cardiac muscle contraction	79	2.298468	0.0049764	0.0001315
hsa04970	Salivary secretion	72	2.282474	0.0050353	0.0001315
hsa05033	Nicotine addiction	35	2.280163	0.0054286	0.0001315
hsa04114	Oocyte meiosis	108	2.236445	0.0047818	0.0001315
hsa00020	Citrate cycle (TCA cycle)	29	2.232058	0.0110237	0.0002169
hsa04720	Long-term potentiation	65	2.231082	0.0050997	0.0001315
hsa04728	Dopaminergic synapse	125	2.211123	0.0047074	0.0001315
hsa03050	Proteasome	43	2.188132	0.0053222	0.0001315
hsa04727	GABAergic synapse	82	2.182124	0.0049599	0.0001315
hsa05017	Spinocerebellar ataxia	124	2.165103	0.0047085	0.0001315
hsa04932	Non-alcoholic fatty liver disease (NAFLD)	139	2.162103	0.0046522	0.0001315
hsa04714	Thermogenesis	220	2.150838	0.0043835	0.0001315
hsa04961	Endocrine and other factor-regulated calcium reabsorption	48	2.137410	0.0052562	0.0001315
hsa04713	Circadian entrainment	93	2.128948	0.0048844	0.0001315
hsa04724	Glutamatergic synapse	108	2.106738	0.0095637	0.0002054
hsa04740	Olfactory transduction	76	2.058759	0.0050016	0.0001315
hsa05031	Amphetamine addiction	63	2.055094	0.0051199	0.0001315
hsa05032	Morphine addiction	85	2.045752	0.0049297	0.0001315
hsa04020	Calcium signaling pathway	184	1.969428	0.0044889	0.0001315
hsa04070	Phosphatidylinositol signaling system	95	1.955506	0.0048702	0.0001315
hsa04925	Aldosterone synthesis and secretion	91	1.940975	0.0097879	0.0002054
hsa04929	GnRH secretion	60	1.932295	0.0412067	0.0006634
hsa04261	Adrenergic signaling in cardiomyocytes	141	1.918299	0.0046345	0.0001315
hsa04921	Oxytocin signaling pathway	149	1.917718	0.0045945	0.0001315
hsa04750	Inflammatory mediator regulation of TRP channels	94	1.881673	0.0195223	0.0003414
hsa04725	Cholinergic synapse	106	1.879938	0.0191920	0.0003414
hsa04910	Insulin signaling pathway	130	1.797130	0.0421438	0.0006634

Enriched terms for module #84AD00 (MTcor = -0.93)
ID	Description	setSize	NES	p.adjust	qvalues
hsa00190	Oxidative phosphorylation	127	2.945789	0.0061467	0.0002020
hsa05016	Huntington disease	289	2.675672	0.0059725	0.0002020
hsa00020	Citrate cycle (TCA cycle)	29	2.597006	0.0063968	0.0002020
hsa05012	Parkinson disease	235	2.585831	0.0060325	0.0002020
hsa04260	Cardiac muscle contraction	79	2.332358	0.0062790	0.0002020
hsa05010	Alzheimer disease	348	2.314316	0.0059151	0.0002020
hsa04721	Synaptic vesicle cycle	70	2.294327	0.0062638	0.0002020
hsa04714	Thermogenesis	220	2.234977	0.0060494	0.0002020
hsa03050	Proteasome	43	2.233015	0.0063597	0.0002020
hsa04932	Non-alcoholic fatty liver disease (NAFLD)	139	2.173141	0.0061074	0.0002020
hsa01210	2-Oxocarboxylic acid metabolism	16	2.134622	0.0259289	0.0006706
hsa01200	Carbon metabolism	109	2.127586	0.0061770	0.0002020
hsa04723	Retrograde endocannabinoid signaling	142	2.098863	0.0061081	0.0002020
hsa04728	Dopaminergic synapse	125	2.012312	0.0061470	0.0002020
hsa04961	Endocrine and other factor-regulated calcium reabsorption	48	2.012073	0.0442044	0.0009997
hsa05017	Spinocerebellar ataxia	124	1.969167	0.0061532	0.0002020
hsa01230	Biosynthesis of amino acids	68	1.967095	0.0376334	0.0009141
hsa04910	Insulin signaling pathway	130	1.918522	0.0061312	0.0002020
hsa04740	Olfactory transduction	76	1.916677	0.0438764	0.0009997
hsa04925	Aldosterone synthesis and secretion	91	1.916531	0.0062171	0.0002020
hsa04261	Adrenergic signaling in cardiomyocytes	141	1.873656	0.0061158	0.0002020
hsa04020	Calcium signaling pathway	184	1.678485	0.0487277	0.0010653

Reactome

print_results(enrichment_Reactome)

Enriched terms for module #73B000 (MTcor = 0.94)
ID	Description	setSize	NES	p.adjust	qvalues
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3	59	3.404989	0.0251148	0.0001590
R-HSA-5334118	DNA methylation	57	3.354489	0.0251134	0.0001590
R-HSA-2299718	Condensation of Prophase Chromosomes	66	3.346491	0.0250763	0.0001590
R-HSA-73728	RNA Polymerase I Promoter Opening	57	3.315263	0.0251134	0.0001590
R-HSA-427359	SIRT1 negatively regulates rRNA expression	62	3.250592	0.0251285	0.0001590
R-HSA-212300	PRC2 methylates histones and DNA	67	3.227406	0.0250861	0.0001590
R-HSA-912446	Meiotic recombination	77	3.195567	0.0250397	0.0001590
R-HSA-1912408	Pre-NOTCH Transcription and Translation	87	3.192122	0.0250673	0.0001590
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	70	3.166086	0.0251176	0.0001590
R-HSA-1912422	Pre-NOTCH Expression and Processing	103	3.120790	0.0250294	0.0001590
R-HSA-8936459	RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function	87	3.120711	0.0250673	0.0001590
R-HSA-5625740	RHO GTPases activate PKNs	87	3.100816	0.0250673	0.0001590
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	83	3.071049	0.0250927	0.0001590
R-HSA-977225	Amyloid fiber formation	92	3.054978	0.0249353	0.0001590
R-HSA-171306	Packaging Of Telomere Ends	45	3.053194	0.0252883	0.0001590
R-HSA-1500620	Meiosis	106	3.047447	0.0249511	0.0001590
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)	103	3.033487	0.0250294	0.0001590
R-HSA-3214815	HDACs deacetylate histones	89	3.027939	0.0250215	0.0001590
R-HSA-110330	Recognition and association of DNA glycosylase with site containing an affected purine	49	3.020401	0.0251918	0.0001590
R-HSA-110331	Cleavage of the damaged purine	49	3.020401	0.0251918	0.0001590
R-HSA-73927	Depurination	49	3.020401	0.0251918	0.0001590
R-HSA-1474165	Reproduction	121	3.018783	0.0249159	0.0001590
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis	105	3.005654	0.0249660	0.0001590
R-HSA-5619507	Activation of HOX genes during differentiation	105	3.005654	0.0249660	0.0001590
R-HSA-73772	RNA Polymerase I Promoter Escape	85	2.995694	0.0250505	0.0001590
R-HSA-9018519	Estrogen-dependent gene expression	139	2.977948	0.0247648	0.0001590
R-HSA-3214842	HDMs demethylate histones	50	2.973280	0.0251648	0.0001590
R-HSA-1221632	Meiotic synapsis	69	2.972464	0.0251148	0.0001590
R-HSA-5250924	B-WICH complex positively regulates rRNA expression	85	2.968917	0.0250505	0.0001590
R-HSA-5578749	Transcriptional regulation by small RNAs	100	2.925635	0.0250196	0.0001590
R-HSA-110328	Recognition and association of DNA glycosylase with site containing an affected pyrimidine	54	2.921933	0.0251435	0.0001590
R-HSA-110329	Cleavage of the damaged pyrimidine	54	2.921933	0.0251435	0.0001590
R-HSA-73928	Depyrimidination	54	2.921933	0.0251435	0.0001590
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere	67	2.897203	0.0250861	0.0001590
R-HSA-774815	Nucleosome assembly	67	2.897203	0.0250861	0.0001590
R-HSA-73929	Base-Excision Repair, AP Site Formation	56	2.892719	0.0251228	0.0001590
R-HSA-3214858	RMTs methylate histone arginines	74	2.859401	0.0251318	0.0001590
R-HSA-427413	NoRC negatively regulates rRNA expression	100	2.815700	0.0250196	0.0001590
R-HSA-68875	Mitotic Prophase	134	2.803678	0.0248199	0.0001590
R-HSA-5250913	Positive epigenetic regulation of rRNA expression	100	2.789580	0.0250196	0.0001590
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence	72	2.789390	0.0251223	0.0001590
R-HSA-5250941	Negative epigenetic regulation of rRNA expression	103	2.768677	0.0250294	0.0001590
R-HSA-73864	RNA Polymerase I Transcription	105	2.759782	0.0249660	0.0001590
R-HSA-73854	RNA Polymerase I Promoter Clearance	104	2.732154	0.0250247	0.0001590
R-HSA-3214841	PKMTs methylate histone lysines	68	2.710487	0.0251059	0.0001590
R-HSA-2559580	Oxidative Stress Induced Senescence	116	2.699026	0.0249135	0.0001590
R-HSA-157579	Telomere Maintenance	74	2.672800	0.0251318	0.0001590
R-HSA-211000	Gene Silencing by RNA	128	2.604248	0.0247987	0.0001590
R-HSA-3214847	HATs acetylate histones	134	2.598060	0.0248199	0.0001590
R-HSA-8939211	ESR-mediated signaling	205	2.590280	0.0244928	0.0001590
R-HSA-73884	Base Excision Repair	84	2.546982	0.0250805	0.0001590
R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs	120	2.515455	0.0249302	0.0001590
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	88	2.497601	0.0250439	0.0001590
R-HSA-73886	Chromosome Maintenance	101	2.483760	0.0249846	0.0001590
R-HSA-2559583	Cellular Senescence	183	2.480288	0.0246088	0.0001590
R-HSA-212165	Epigenetic regulation of gene expression	140	2.462506	0.0247974	0.0001590
R-HSA-5693571	Nonhomologous End-Joining (NHEJ)	66	2.460174	0.0250763	0.0001590
R-HSA-6783783	Interleukin-10 signaling	34	2.418768	0.0252845	0.0001590
R-HSA-5693565	Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks	73	2.396526	0.0251252	0.0001590
R-HSA-5693606	DNA Double Strand Break Response	74	2.396061	0.0251318	0.0001590
R-HSA-9006931	Signaling by Nuclear Receptors	244	2.381399	0.0243898	0.0001590
R-HSA-1566948	Elastic fibre formation	43	2.370406	0.0252611	0.0001590
R-HSA-8941326	RUNX2 regulates bone development	30	2.351001	0.0252954	0.0001590
R-HSA-69473	G2/M DNA damage checkpoint	91	2.341737	0.0249683	0.0001590
R-HSA-5693607	Processing of DNA double-strand break ends	94	2.341501	0.0249725	0.0001590
R-HSA-1474244	Extracellular matrix organization	263	2.331853	0.0243579	0.0001590
R-HSA-1266695	Interleukin-7 signaling	33	2.306149	0.0253327	0.0001590
R-HSA-3247509	Chromatin modifying enzymes	259	2.278873	0.0243207	0.0001590
R-HSA-4839726	Chromatin organization	259	2.278873	0.0243207	0.0001590
R-HSA-5693567	HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)	126	2.235138	0.0248641	0.0001590
R-HSA-157118	Signaling by NOTCH	224	2.214671	0.0244334	0.0001590
R-HSA-8878171	Transcriptional regulation by RUNX1	218	2.201971	0.0244490	0.0001590
R-HSA-5693538	Homology Directed Repair	132	2.171556	0.0248447	0.0001590
R-HSA-3000170	Syndecan interactions	27	2.155250	0.0253136	0.0001590
R-HSA-3108232	SUMO E3 ligases SUMOylate target proteins	175	2.093088	0.0245655	0.0001590
R-HSA-1474290	Collagen formation	84	2.086264	0.0250805	0.0001590
R-HSA-201681	TCF dependent signaling in response to WNT	215	2.034284	0.0244125	0.0001590
R-HSA-2990846	SUMOylation	181	2.007948	0.0245606	0.0001590
R-HSA-5693532	DNA Double-Strand Break Repair	160	1.923506	0.0246523	0.0001590
R-HSA-195258	RHO GTPase Effectors	304	1.840488	0.0241978	0.0001590
R-HSA-449147	Signaling by Interleukins	393	1.805721	0.0238851	0.0001590
R-HSA-195721	Signaling by WNT	309	1.690092	0.0484043	0.0002494
R-HSA-68886	M Phase	370	1.647770	0.0479453	0.0002489
R-HSA-2262752	Cellular responses to stress	405	1.632674	0.0477761	0.0002489

Enriched terms for module #EE8045 (MTcor = 0.93)
ID	Description	setSize	NES	p.adjust	qvalues
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3	59	3.428710	0.0224452	0.0001374
R-HSA-5334118	DNA methylation	57	3.406522	0.0225278	0.0001374
R-HSA-73728	RNA Polymerase I Promoter Opening	57	3.355613	0.0225278	0.0001374
R-HSA-2299718	Condensation of Prophase Chromosomes	66	3.267881	0.0222082	0.0001374
R-HSA-427359	SIRT1 negatively regulates rRNA expression	62	3.259000	0.0223359	0.0001374
R-HSA-212300	PRC2 methylates histones and DNA	67	3.195257	0.0221954	0.0001374
R-HSA-3214815	HDACs deacetylate histones	89	3.183673	0.0217741	0.0001374
R-HSA-912446	Meiotic recombination	77	3.177327	0.0220402	0.0001374
R-HSA-1912408	Pre-NOTCH Transcription and Translation	87	3.167742	0.0218376	0.0001374
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	70	3.166898	0.0221338	0.0001374
R-HSA-8936459	RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function	87	3.142486	0.0218376	0.0001374
R-HSA-5625740	RHO GTPases activate PKNs	87	3.092663	0.0218376	0.0001374
R-HSA-1500620	Meiosis	106	3.041621	0.0214335	0.0001374
R-HSA-171306	Packaging Of Telomere Ends	45	3.029616	0.0228412	0.0001374
R-HSA-73772	RNA Polymerase I Promoter Escape	85	3.024781	0.0218633	0.0001374
R-HSA-1221632	Meiotic synapsis	69	3.021587	0.0221711	0.0001374
R-HSA-1912422	Pre-NOTCH Expression and Processing	103	2.995518	0.0214362	0.0001374
R-HSA-1474165	Reproduction	121	2.990888	0.0211577	0.0001374
R-HSA-977225	Amyloid fiber formation	92	2.976874	0.0216948	0.0001374
R-HSA-110330	Recognition and association of DNA glycosylase with site containing an affected purine	49	2.955917	0.0227469	0.0001374
R-HSA-110331	Cleavage of the damaged purine	49	2.955917	0.0227469	0.0001374
R-HSA-73927	Depurination	49	2.955917	0.0227469	0.0001374
R-HSA-5250924	B-WICH complex positively regulates rRNA expression	85	2.945840	0.0218633	0.0001374
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	83	2.931072	0.0218740	0.0001374
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)	103	2.919696	0.0214362	0.0001374
R-HSA-427413	NoRC negatively regulates rRNA expression	100	2.872722	0.0214971	0.0001374
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis	105	2.867060	0.0214081	0.0001374
R-HSA-5619507	Activation of HOX genes during differentiation	105	2.867060	0.0214081	0.0001374
R-HSA-5578749	Transcriptional regulation by small RNAs	100	2.865456	0.0214971	0.0001374
R-HSA-9018519	Estrogen-dependent gene expression	139	2.861305	0.0208499	0.0001374
R-HSA-110328	Recognition and association of DNA glycosylase with site containing an affected pyrimidine	54	2.857918	0.0225696	0.0001374
R-HSA-110329	Cleavage of the damaged pyrimidine	54	2.857918	0.0225696	0.0001374
R-HSA-73928	Depyrimidination	54	2.857918	0.0225696	0.0001374
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence	72	2.845834	0.0220842	0.0001374
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere	67	2.832629	0.0221954	0.0001374
R-HSA-774815	Nucleosome assembly	67	2.832629	0.0221954	0.0001374
R-HSA-73929	Base-Excision Repair, AP Site Formation	56	2.824304	0.0225502	0.0001374
R-HSA-5250941	Negative epigenetic regulation of rRNA expression	103	2.813435	0.0214362	0.0001374
R-HSA-3214842	HDMs demethylate histones	50	2.792860	0.0227196	0.0001374
R-HSA-73864	RNA Polymerase I Transcription	105	2.772099	0.0214081	0.0001374
R-HSA-73854	RNA Polymerase I Promoter Clearance	104	2.753275	0.0214122	0.0001374
R-HSA-5250913	Positive epigenetic regulation of rRNA expression	100	2.745753	0.0214971	0.0001374
R-HSA-3214858	RMTs methylate histone arginines	74	2.745707	0.0220896	0.0001374
R-HSA-3214847	HATs acetylate histones	134	2.695651	0.0209365	0.0001374
R-HSA-68875	Mitotic Prophase	134	2.687889	0.0209365	0.0001374
R-HSA-157579	Telomere Maintenance	74	2.678335	0.0220896	0.0001374
R-HSA-5693565	Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks	73	2.669142	0.0220969	0.0001374
R-HSA-5693606	DNA Double Strand Break Response	74	2.658132	0.0220896	0.0001374
R-HSA-211000	Gene Silencing by RNA	128	2.636333	0.0209926	0.0001374
R-HSA-5693571	Nonhomologous End-Joining (NHEJ)	66	2.633793	0.0222082	0.0001374
R-HSA-3214841	PKMTs methylate histone lysines	68	2.560910	0.0221843	0.0001374
R-HSA-212165	Epigenetic regulation of gene expression	140	2.555835	0.0208463	0.0001374
R-HSA-2559580	Oxidative Stress Induced Senescence	116	2.542884	0.0212351	0.0001374
R-HSA-73886	Chromosome Maintenance	101	2.490931	0.0215019	0.0001374
R-HSA-73884	Base Excision Repair	84	2.481520	0.0218801	0.0001374
R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs	120	2.458849	0.0211600	0.0001374
R-HSA-8939211	ESR-mediated signaling	205	2.449368	0.0200212	0.0001374
R-HSA-69473	G2/M DNA damage checkpoint	91	2.394096	0.0217515	0.0001374
R-HSA-5693607	Processing of DNA double-strand break ends	94	2.388162	0.0216587	0.0001374
R-HSA-3247509	Chromatin modifying enzymes	259	2.382042	0.0195119	0.0001374
R-HSA-4839726	Chromatin organization	259	2.382042	0.0195119	0.0001374
R-HSA-1474290	Collagen formation	84	2.337750	0.0218801	0.0001374
R-HSA-2559583	Cellular Senescence	183	2.295883	0.0202788	0.0001374
R-HSA-8878171	Transcriptional regulation by RUNX1	218	2.261105	0.0198763	0.0001374
R-HSA-2022090	Assembly of collagen fibrils and other multimeric structures	56	2.236997	0.0225502	0.0001374
R-HSA-5693567	HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)	126	2.229659	0.0210738	0.0001374
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	88	2.229070	0.0218120	0.0001374
R-HSA-9006931	Signaling by Nuclear Receptors	244	2.206897	0.0196781	0.0001374
R-HSA-1474244	Extracellular matrix organization	263	2.206092	0.0194762	0.0001374
R-HSA-1650814	Collagen biosynthesis and modifying enzymes	65	2.192422	0.0222185	0.0001374
R-HSA-5693538	Homology Directed Repair	132	2.149519	0.0210048	0.0001374
R-HSA-216083	Integrin cell surface interactions	75	2.089222	0.0220449	0.0001374
R-HSA-3108232	SUMO E3 ligases SUMOylate target proteins	175	2.071740	0.0203379	0.0001374
R-HSA-4551638	SUMOylation of chromatin organization proteins	70	2.046488	0.0442675	0.0001501
R-HSA-5693532	DNA Double-Strand Break Repair	160	2.018206	0.0205764	0.0001374
R-HSA-2990846	SUMOylation	181	1.979695	0.0202852	0.0001374
R-HSA-157118	Signaling by NOTCH	224	1.951114	0.0198181	0.0001374
R-HSA-1474228	Degradation of the extracellular matrix	117	1.880459	0.0424171	0.0001454
R-HSA-195258	RHO GTPase Effectors	304	1.829443	0.0191205	0.0001374
R-HSA-194315	Signaling by Rho GTPases	427	1.815317	0.0183115	0.0001374
R-HSA-201681	TCF dependent signaling in response to WNT	215	1.685616	0.0398614	0.0001399
R-HSA-449147	Signaling by Interleukins	393	1.646806	0.0185323	0.0001374
R-HSA-68886	M Phase	370	1.603246	0.0186825	0.0001374

Enriched terms for module #00B9E3 (MTcor = -0.93)
ID	Description	setSize	NES	p.adjust	qvalues
R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	122	2.771562	0.0197786	0.0003057
R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	170	2.722842	0.0189276	0.0003057
R-HSA-611105	Respiratory electron transport	100	2.712848	0.0202396	0.0003057
R-HSA-112316	Neuronal System	379	2.643595	0.0169280	0.0003057
R-HSA-112315	Transmission across Chemical Synapses	245	2.572379	0.0179982	0.0003057
R-HSA-180024	DARPP-32 events	25	2.566180	0.0231774	0.0003057
R-HSA-5576892	Phase 0 - rapid depolarisation	45	2.542660	0.0219888	0.0003057
R-HSA-1296072	Voltage gated Potassium channels	40	2.533345	0.0222219	0.0003057
R-HSA-399719	Trafficking of AMPA receptors	30	2.525597	0.0228369	0.0003057
R-HSA-399721	Glutamate binding, activation of AMPA receptors and synaptic plasticity	30	2.525597	0.0228369	0.0003057
R-HSA-112314	Neurotransmitter receptors and postsynaptic signal transmission	184	2.501833	0.0187214	0.0003057
R-HSA-6799198	Complex I biogenesis	55	2.486575	0.0215979	0.0003057
R-HSA-442755	Activation of NMDA receptors and postsynaptic events	84	2.413330	0.0206268	0.0003057
R-HSA-438066	Unblocking of NMDA receptors, glutamate binding and activation	22	2.398864	0.0233726	0.0003057
R-HSA-445095	Interaction between L1 and Ankyrins	29	2.389660	0.0228525	0.0003057
R-HSA-442982	Ras activation upon Ca2+ influx through NMDA receptor	21	2.358380	0.0234935	0.0003057
R-HSA-9620244	Long-term potentiation	24	2.331833	0.0231806	0.0003057
R-HSA-9617324	Negative regulation of NMDA receptor-mediated neuronal transmission	22	2.316670	0.0233726	0.0003057
R-HSA-438064	Post NMDA receptor activation events	73	2.314038	0.0210213	0.0003057
R-HSA-5682910	LGI-ADAM interactions	14	2.302572	0.0241829	0.0003057
R-HSA-416993	Trafficking of GluR2-containing AMPA receptors	16	2.294111	0.0239491	0.0003057
R-HSA-6794362	Protein-protein interactions at synapses	87	2.281273	0.0205509	0.0003057
R-HSA-1489509	DAG and IP3 signaling	41	2.253555	0.0221843	0.0003057
R-HSA-111933	Calmodulin induced events	35	2.244918	0.0224995	0.0003057
R-HSA-111997	CaM pathway	35	2.244918	0.0224995	0.0003057
R-HSA-8849932	Synaptic adhesion-like molecules	21	2.236925	0.0469870	0.0004354
R-HSA-1296071	Potassium Channels	92	2.209534	0.0204446	0.0003057
R-HSA-168799	Neurotoxicity of clostridium toxins	10	2.193865	0.0494018	0.0004437
R-HSA-442742	CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling	29	2.190215	0.0228525	0.0003057
R-HSA-5576891	Cardiac conduction	131	2.186421	0.0196061	0.0003057
R-HSA-5339562	Uptake and actions of bacterial toxins	30	2.186355	0.0228369	0.0003057
R-HSA-111885	Opioid Signalling	86	2.173169	0.0205528	0.0003057
R-HSA-111996	Ca-dependent events	37	2.168548	0.0447450	0.0004302
R-HSA-1168372	Downstream signaling events of B Cell Receptor (BCR)	81	2.166032	0.0207344	0.0003057
R-HSA-888590	GABA synthesis, release, reuptake and degradation	19	2.161818	0.0472005	0.0004354
R-HSA-442720	CREB1 phosphorylation through the activation of Adenylate Cyclase	13	2.151123	0.0484717	0.0004412
R-HSA-1236978	Cross-presentation of soluble exogenous antigens (endosomes)	47	2.149661	0.0219284	0.0003057
R-HSA-210500	Glutamate Neurotransmitter Release Cycle	24	2.146751	0.0463612	0.0004354
R-HSA-69052	Switching of origins to a post-replicative state	87	2.142347	0.0205509	0.0003057
R-HSA-5578775	Ion homeostasis	53	2.140474	0.0216580	0.0003057
R-HSA-68827	CDT1 association with the CDC6:ORC:origin complex	57	2.130876	0.0215175	0.0003057
R-HSA-68867	Assembly of the pre-replicative complex	65	2.128218	0.0212570	0.0003057
R-HSA-5610783	Degradation of GLI2 by the proteasome	57	2.115002	0.0215175	0.0003057
R-HSA-112310	Neurotransmitter release cycle	47	2.106833	0.0219284	0.0003057
R-HSA-8986944	Transcriptional Regulation by MECP2	61	2.090800	0.0213952	0.0003057
R-HSA-5610785	GLI3 is processed to GLI3R by the proteasome	57	2.082944	0.0215175	0.0003057
R-HSA-2454202	Fc epsilon receptor (FCERI) signaling	129	2.079485	0.0196412	0.0003057
R-HSA-68949	Orc1 removal from chromatin	69	2.077892	0.0210941	0.0003057
R-HSA-5610780	Degradation of GLI1 by the proteasome	57	2.075156	0.0215175	0.0003057
R-HSA-5676590	NIK–>noncanonical NF-kB signaling	56	2.066272	0.0215590	0.0003057
R-HSA-174113	SCF-beta-TrCP mediated degradation of Emi1	53	2.034135	0.0216580	0.0003057
R-HSA-8939902	Regulation of RUNX2 expression and activity	70	2.018323	0.0421516	0.0004217
R-HSA-174084	Autodegradation of Cdh1 by Cdh1:APC/C	62	2.018057	0.0427044	0.0004217
R-HSA-176408	Regulation of APC/C activators between G1/S and early anaphase	76	2.013606	0.0418253	0.0004217
R-HSA-6794361	Neurexins and neuroligins	56	2.008824	0.0431180	0.0004217
R-HSA-5607761	Dectin-1 mediated noncanonical NF-kB signaling	57	2.008410	0.0430349	0.0004217
R-HSA-5610787	Hedgehog ‘off’ state	108	2.001968	0.0200302	0.0003057
R-HSA-9604323	Negative regulation of NOTCH4 signaling	54	1.999309	0.0432453	0.0004217
R-HSA-983705	Signaling by the B Cell Receptor (BCR)	107	1.998265	0.0200599	0.0003057
R-HSA-69017	CDK-mediated phosphorylation and removal of Cdc6	69	1.989499	0.0421881	0.0004217
R-HSA-373760	L1CAM interactions	111	1.940906	0.0399737	0.0004217
R-HSA-5607764	CLEC7A (Dectin-1) signaling	98	1.921267	0.0406331	0.0004217
R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	296	1.889138	0.0175230	0.0003057
R-HSA-5673001	RAF/MAP kinase cascade	224	1.863297	0.0181937	0.0003057
R-HSA-397014	Muscle contraction	187	1.841178	0.0187025	0.0003057
R-HSA-5684996	MAPK1/MAPK3 signaling	230	1.806671	0.0181680	0.0003057
R-HSA-8951664	Neddylation	225	1.772501	0.0363849	0.0004217
R-HSA-5683057	MAPK family signaling cascades	266	1.739480	0.0177747	0.0003057
R-HSA-1852241	Organelle biogenesis and maintenance	286	1.730102	0.0176001	0.0003057
R-HSA-69620	Cell Cycle Checkpoints	279	1.688245	0.0176632	0.0003057

Enriched terms for module #84AD00 (MTcor = -0.93)
ID	Description	setSize	NES	p.adjust	qvalues
R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	170	3.030448	0.0256882	0.0002955
R-HSA-611105	Respiratory electron transport	100	2.953639	0.0261010	0.0002955
R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	122	2.931129	0.0258897	0.0002955
R-HSA-5576892	Phase 0 - rapid depolarisation	45	2.640552	0.0265488	0.0002955
R-HSA-6799198	Complex I biogenesis	55	2.632292	0.0265415	0.0002955
R-HSA-888590	GABA synthesis, release, reuptake and degradation	19	2.531137	0.0269022	0.0002955
R-HSA-71406	Pyruvate metabolism and Citric Acid (TCA) cycle	52	2.519440	0.0265678	0.0002955
R-HSA-71403	Citric acid cycle (TCA cycle)	22	2.480228	0.0268220	0.0002955
R-HSA-112316	Neuronal System	379	2.473304	0.0247369	0.0002955
R-HSA-1296072	Voltage gated Potassium channels	40	2.452507	0.0265594	0.0002955
R-HSA-399719	Trafficking of AMPA receptors	30	2.429160	0.0266492	0.0002955
R-HSA-399721	Glutamate binding, activation of AMPA receptors and synaptic plasticity	30	2.429160	0.0266492	0.0002955
R-HSA-1268020	Mitochondrial protein import	63	2.427393	0.0263920	0.0002955
R-HSA-5682910	LGI-ADAM interactions	14	2.425477	0.0269563	0.0002955
R-HSA-112315	Transmission across Chemical Synapses	245	2.416597	0.0253870	0.0002955
R-HSA-180024	DARPP-32 events	25	2.406851	0.0267465	0.0002955
R-HSA-442982	Ras activation upon Ca2+ influx through NMDA receptor	21	2.375977	0.0268801	0.0002955
R-HSA-5339562	Uptake and actions of bacterial toxins	30	2.311167	0.0266492	0.0002955
R-HSA-112310	Neurotransmitter release cycle	47	2.301053	0.0265631	0.0002955
R-HSA-442755	Activation of NMDA receptors and postsynaptic events	84	2.242816	0.0262123	0.0002955
R-HSA-5389840	Mitochondrial translation elongation	86	2.235272	0.0262236	0.0002955
R-HSA-112314	Neurotransmitter receptors and postsynaptic signal transmission	184	2.229291	0.0255794	0.0002955
R-HSA-111933	Calmodulin induced events	35	2.223602	0.0266275	0.0002955
R-HSA-111997	CaM pathway	35	2.223602	0.0266275	0.0002955
R-HSA-5368287	Mitochondrial translation	92	2.210952	0.0261086	0.0002955
R-HSA-5368286	Mitochondrial translation initiation	86	2.170356	0.0262236	0.0002955
R-HSA-5419276	Mitochondrial translation termination	86	2.166536	0.0262236	0.0002955
R-HSA-351202	Metabolism of polyamines	83	2.144309	0.0261657	0.0002955
R-HSA-111885	Opioid Signalling	86	2.136095	0.0262236	0.0002955
R-HSA-438064	Post NMDA receptor activation events	73	2.114563	0.0262900	0.0002955
R-HSA-1296071	Potassium Channels	92	2.093680	0.0261086	0.0002955
R-HSA-9609507	Protein localization	158	2.020541	0.0258224	0.0002955
R-HSA-5628897	TP53 Regulates Metabolic Genes	84	1.970919	0.0262123	0.0002955
R-HSA-8951664	Neddylation	225	1.969353	0.0254564	0.0002955
R-HSA-5576891	Cardiac conduction	131	1.937803	0.0258647	0.0002955
R-HSA-163685	Integration of energy metabolism	101	1.905819	0.0260721	0.0002955
R-HSA-8856688	Golgi-to-ER retrograde transport	124	1.869820	0.0258747	0.0002955
R-HSA-5610787	Hedgehog ‘off’ state	108	1.864307	0.0259791	0.0002955
R-HSA-1852241	Organelle biogenesis and maintenance	286	1.728487	0.0252216	0.0002955

Gene Ontology

print_results(enrichment_GO)

No enrichment found for module #73B000

No enrichment found for module #EE8045

No enrichment found for module #00B9E3

No enrichment found for module #84AD00

Disease Ontology

print_results(enrichment_DO)

Enriched terms for module #73B000 (MTcor = 0.94)
ID	Description	setSize	NES	p.adjust	qvalues
DOID:1936	atherosclerosis	280	2.328354	0.0141355	0.0000646
DOID:1115	sarcoma	173	2.326923	0.0143437	0.0000646
DOID:2348	arteriosclerotic cardiovascular disease	281	2.319477	0.0141406	0.0000646
DOID:2349	arteriosclerosis	287	2.304857	0.0141348	0.0000646
DOID:2213	hemorrhagic disease	121	2.270698	0.0145040	0.0000646
DOID:0050161	lower respiratory tract disease	391	2.258512	0.0139636	0.0000646
DOID:552	pneumonia	78	2.257550	0.0146515	0.0000646
DOID:3770	pulmonary fibrosis	101	2.254562	0.0145592	0.0000646
DOID:1579	respiratory system disease	429	2.239237	0.0138906	0.0000646
DOID:850	lung disease	383	2.238401	0.0139628	0.0000646
DOID:3083	chronic obstructive pulmonary disease	174	2.222449	0.0143482	0.0000646
DOID:3717	gastric adenocarcinoma	81	2.214898	0.0146567	0.0000646
DOID:2218	blood platelet disease	76	2.212813	0.0146649	0.0000646
DOID:5520	head and neck squamous cell carcinoma	153	2.211620	0.0143988	0.0000646
DOID:3082	interstitial lung disease	136	2.199707	0.0145166	0.0000646
DOID:2320	obstructive lung disease	229	2.198971	0.0142248	0.0000646
DOID:7148	rheumatoid arthritis	430	2.196661	0.0138820	0.0000646
DOID:10534	stomach cancer	231	2.187767	0.0142008	0.0000646
DOID:13133	HELLP syndrome	15	2.169495	0.0300954	0.0001198
DOID:4330	non-langerhans-cell histiocytosis	11	2.167417	0.0300395	0.0001198
DOID:520	aortic disease	48	2.155743	0.0295192	0.0001198
DOID:1247	blood coagulation disease	142	2.155103	0.0144770	0.0000646
DOID:11934	head and neck cancer	209	2.151208	0.0142719	0.0000646
DOID:104	bacterial infectious disease	191	2.144434	0.0143042	0.0000646
DOID:14504	Niemann-Pick disease	10	2.141539	0.0300544	0.0001198
DOID:3627	aortic aneurysm	47	2.130650	0.0443138	0.0001681
DOID:1542	head and neck carcinoma	206	2.128565	0.0143157	0.0000646
DOID:37	skin disease	254	2.125717	0.0141908	0.0000646
DOID:1793	pancreatic cancer	276	2.111636	0.0141465	0.0000646
DOID:1588	thrombocytopenia	57	2.110410	0.0294471	0.0001198
DOID:4362	cervical cancer	96	2.106032	0.0145975	0.0000646
DOID:1520	colon carcinoma	149	2.105316	0.0144346	0.0000646
DOID:409	liver disease	500	2.104661	0.0137786	0.0000646
DOID:5517	stomach carcinoma	133	2.103167	0.0145019	0.0000646
DOID:201	connective tissue cancer	338	2.099796	0.0140341	0.0000646
DOID:4905	pancreatic carcinoma	206	2.098585	0.0143157	0.0000646
DOID:4481	allergic rhinitis	67	2.096063	0.0146891	0.0000646
DOID:1176	bronchial disease	104	2.091506	0.0145449	0.0000646
DOID:824	periodontitis	88	2.090860	0.0146400	0.0000646
DOID:3326	purpura	57	2.087347	0.0294471	0.0001198
DOID:2893	cervix carcinoma	95	2.083596	0.0145964	0.0000646
DOID:2163	nasal cavity disease	69	2.078487	0.0147015	0.0000646
DOID:2825	nose disease	69	2.078487	0.0147015	0.0000646
DOID:4483	rhinitis	69	2.078487	0.0147015	0.0000646
DOID:3388	periodontal disease	99	2.072415	0.0145655	0.0000646
DOID:0050338	primary bacterial infectious disease	165	2.071690	0.0144081	0.0000646
DOID:170	endocrine gland cancer	443	2.066980	0.0138445	0.0000646
DOID:854	collagen disease	159	2.056954	0.0144179	0.0000646
DOID:10124	corneal disease	46	2.055284	0.0443707	0.0001681
DOID:2151	malignant ovarian surface epithelial-stromal neoplasm	256	2.041443	0.0142160	0.0000646
DOID:2152	ovary epithelial cancer	256	2.041443	0.0142160	0.0000646
DOID:4001	ovarian carcinoma	256	2.041443	0.0142160	0.0000646
DOID:0060100	musculoskeletal system cancer	395	2.035164	0.0139410	0.0000646
DOID:219	colon cancer	252	2.034711	0.0142155	0.0000646
DOID:0060058	lymphoma	66	2.031428	0.0146775	0.0000646
DOID:9256	colorectal cancer	256	2.031151	0.0142160	0.0000646
DOID:3310	atopic dermatitis	92	2.031063	0.0145779	0.0000646
DOID:120	female reproductive organ cancer	393	2.029211	0.0139514	0.0000646
DOID:5672	large intestine cancer	257	2.029211	0.0141949	0.0000646
DOID:4960	bone marrow cancer	274	2.021302	0.0141557	0.0000646
DOID:9538	multiple myeloma	221	2.020293	0.0142745	0.0000646
DOID:16	integumentary system disease	288	2.020174	0.0141139	0.0000646
DOID:6713	cerebrovascular disease	98	2.015214	0.0145836	0.0000646
DOID:1091	tooth disease	114	2.013934	0.0145609	0.0000646
DOID:2237	hepatitis	345	2.011724	0.0140208	0.0000646
DOID:0070004	myeloma	269	2.010450	0.0141805	0.0000646
DOID:399	tuberculosis	106	2.009155	0.0145344	0.0000646
DOID:3910	lung adenocarcinoma	153	1.998887	0.0143988	0.0000646
DOID:2394	ovarian cancer	276	1.993121	0.0141465	0.0000646
DOID:2916	hypersensitivity reaction type IV disease	70	1.987438	0.0440994	0.0001681
DOID:1612	breast cancer	451	1.987036	0.0138379	0.0000646
DOID:5093	thoracic cancer	451	1.987036	0.0138379	0.0000646
DOID:1575	rheumatic disease	147	1.985583	0.0144391	0.0000646
DOID:418	systemic scleroderma	147	1.985583	0.0144391	0.0000646
DOID:419	scleroderma	147	1.985583	0.0144391	0.0000646
DOID:10155	intestinal cancer	268	1.978959	0.0141867	0.0000646
DOID:5082	liver cirrhosis	173	1.977049	0.0143437	0.0000646
DOID:3908	non-small cell lung carcinoma	370	1.971734	0.0139860	0.0000646
DOID:3905	lung carcinoma	441	1.967848	0.0138396	0.0000646
DOID:11054	urinary bladder cancer	90	1.964252	0.0146427	0.0000646
DOID:10283	prostate cancer	364	1.960564	0.0140005	0.0000646
DOID:2043	hepatitis B	160	1.945112	0.0144059	0.0000646
DOID:4074	pancreas adenocarcinoma	142	1.942827	0.0144770	0.0000646
DOID:1040	chronic lymphocytic leukemia	167	1.934531	0.0143951	0.0000646
DOID:2723	dermatitis	123	1.928381	0.0145148	0.0000646
DOID:974	upper respiratory tract disease	86	1.928198	0.0437573	0.0001681
DOID:5041	esophageal cancer	127	1.904152	0.0145341	0.0000646
DOID:8398	osteoarthritis	158	1.902832	0.0144264	0.0000646
DOID:8692	myeloid leukemia	124	1.902192	0.0145242	0.0000646
DOID:2841	asthma	91	1.898807	0.0292472	0.0001198
DOID:10952	nephritis	118	1.888222	0.0290483	0.0001198
DOID:417	hypersensitivity reaction type II disease	444	1.887243	0.0138447	0.0000646
DOID:403	mouth disease	136	1.887171	0.0290333	0.0001198
DOID:3856	male reproductive organ cancer	372	1.886447	0.0139778	0.0000646
DOID:184	bone cancer	224	1.885886	0.0142564	0.0000646
DOID:3393	coronary artery disease	268	1.885598	0.0141867	0.0000646
DOID:3347	osteosarcoma	204	1.880283	0.0142974	0.0000646
DOID:688	embryonal cancer	316	1.871146	0.0140769	0.0000646
DOID:114	heart disease	420	1.870466	0.0138783	0.0000646
DOID:5844	myocardial infarction	220	1.868891	0.0142691	0.0000646
DOID:3459	breast carcinoma	339	1.854647	0.0140220	0.0000646
DOID:4451	renal carcinoma	328	1.853181	0.0140582	0.0000646
DOID:1883	hepatitis C	190	1.846083	0.0143147	0.0000646
DOID:4195	hyperglycemia	110	1.840590	0.0436801	0.0001681
DOID:2994	germ cell cancer	343	1.836173	0.0140100	0.0000646
DOID:3996	urinary system cancer	426	1.831902	0.0138683	0.0000646
DOID:9352	type 2 diabetes mellitus	166	1.831581	0.0288363	0.0001198
DOID:1492	eye and adnexa disease	441	1.829360	0.0138396	0.0000646
DOID:4766	embryoma	298	1.828122	0.0141147	0.0000646
DOID:5614	eye disease	432	1.813335	0.0138781	0.0000646
DOID:0050155	sensory system disease	489	1.786407	0.0138079	0.0000646
DOID:557	kidney disease	374	1.766649	0.0139798	0.0000646
DOID:0060072	benign neoplasm	474	1.760866	0.0138142	0.0000646
DOID:263	kidney cancer	375	1.760670	0.0139738	0.0000646
DOID:4450	renal cell carcinoma	294	1.752802	0.0141368	0.0000646
DOID:1037	lymphoblastic leukemia	359	1.746446	0.0140083	0.0000646
DOID:18	urinary system disease	387	1.742797	0.0139544	0.0000646
DOID:0060084	cell type benign neoplasm	396	1.717393	0.0139259	0.0000646
DOID:74	hematopoietic system disease	366	1.664221	0.0140083	0.0000646
DOID:657	adenoma	278	1.656929	0.0424373	0.0001676
DOID:0050736	autosomal dominant disease	360	1.620271	0.0140068	0.0000646
DOID:3093	nervous system cancer	499	1.618691	0.0137836	0.0000646
DOID:10763	hypertension	482	1.580088	0.0275518	0.0001198

Enriched terms for module #EE8045 (MTcor = 0.93)
ID	Description	setSize	NES	p.adjust	qvalues
DOID:7148	rheumatoid arthritis	430	2.406930	0.0106781	0.0000717
DOID:3083	chronic obstructive pulmonary disease	174	2.354784	0.0119021	0.0000717
DOID:2213	hemorrhagic disease	121	2.315706	0.0123496	0.0000717
DOID:1588	thrombocytopenia	57	2.284217	0.0130870	0.0000717
DOID:3770	pulmonary fibrosis	101	2.278557	0.0125472	0.0000717
DOID:0050161	lower respiratory tract disease	391	2.276961	0.0108113	0.0000717
DOID:1579	respiratory system disease	429	2.273814	0.0106829	0.0000717
DOID:2320	obstructive lung disease	229	2.272892	0.0115597	0.0000717
DOID:850	lung disease	383	2.266257	0.0108398	0.0000717
DOID:1247	blood coagulation disease	142	2.265142	0.0121645	0.0000717
DOID:9446	cholangitis	25	2.255001	0.0138001	0.0000749
DOID:3388	periodontal disease	99	2.231499	0.0125639	0.0000717
DOID:3082	interstitial lung disease	136	2.231101	0.0122120	0.0000717
DOID:0060049	autoimmune disease of urogenital tract	56	2.217154	0.0130863	0.0000717
DOID:12236	primary biliary cirrhosis	56	2.217154	0.0130863	0.0000717
DOID:9074	systemic lupus erythematosus	58	2.217005	0.0130850	0.0000717
DOID:1115	sarcoma	173	2.209575	0.0118957	0.0000717
DOID:3326	purpura	57	2.205286	0.0261739	0.0001338
DOID:2218	blood platelet disease	76	2.203795	0.0128457	0.0000717
DOID:4481	allergic rhinitis	67	2.201114	0.0129694	0.0000717
DOID:1040	chronic lymphocytic leukemia	167	2.196968	0.0119612	0.0000717
DOID:2163	nasal cavity disease	69	2.192375	0.0129535	0.0000717
DOID:2825	nose disease	69	2.192375	0.0129535	0.0000717
DOID:4483	rhinitis	69	2.192375	0.0129535	0.0000717
DOID:824	periodontitis	88	2.192074	0.0126812	0.0000717
DOID:2916	hypersensitivity reaction type IV disease	70	2.178799	0.0129258	0.0000717
DOID:8857	lupus erythematosus	62	2.165345	0.0130310	0.0000717
DOID:974	upper respiratory tract disease	86	2.150957	0.0127097	0.0000717
DOID:1091	tooth disease	114	2.150849	0.0124174	0.0000717
DOID:11335	sarcoidosis	66	2.149124	0.0259538	0.0001338
DOID:8398	osteoarthritis	158	2.148051	0.0120238	0.0000717
DOID:1176	bronchial disease	104	2.147108	0.0124946	0.0000717
DOID:1936	atherosclerosis	280	2.132366	0.0112663	0.0000717
DOID:2348	arteriosclerotic cardiovascular disease	281	2.129309	0.0112619	0.0000717
DOID:2473	opportunistic mycosis	27	2.125544	0.0411613	0.0001937
DOID:10952	nephritis	118	2.119637	0.0123714	0.0000717
DOID:2349	arteriosclerosis	287	2.118736	0.0112205	0.0000717
DOID:552	pneumonia	78	2.099390	0.0128142	0.0000717
DOID:2841	asthma	91	2.077346	0.0126525	0.0000717
DOID:8692	myeloid leukemia	124	2.072009	0.0123179	0.0000717
DOID:612	primary immunodeficiency disease	158	2.064591	0.0120238	0.0000717
DOID:11934	head and neck cancer	209	2.061705	0.0116792	0.0000717
DOID:1542	head and neck carcinoma	206	2.054663	0.0116903	0.0000717
DOID:0060058	lymphoma	66	2.051627	0.0389307	0.0001848
DOID:399	tuberculosis	106	2.049425	0.0125026	0.0000717
DOID:9538	multiple myeloma	221	2.039118	0.0116078	0.0000717
DOID:9741	biliary tract disease	71	2.036162	0.0387428	0.0001848
DOID:104	bacterial infectious disease	191	2.030575	0.0117797	0.0000717
DOID:12361	Graves’ disease	63	2.028658	0.0260517	0.0001338
DOID:5082	liver cirrhosis	173	2.025518	0.0118957	0.0000717
DOID:5520	head and neck squamous cell carcinoma	153	2.018823	0.0120762	0.0000717
DOID:11054	urinary bladder cancer	90	2.014636	0.0126652	0.0000717
DOID:4138	bile duct disease	70	2.007146	0.0387773	0.0001848
DOID:37	skin disease	254	1.996581	0.0114104	0.0000717
DOID:417	hypersensitivity reaction type II disease	444	1.993203	0.0106488	0.0000717
DOID:4960	bone marrow cancer	274	1.990757	0.0112936	0.0000717
DOID:0070004	myeloma	269	1.988499	0.0113169	0.0000717
DOID:403	mouth disease	136	1.988237	0.0122120	0.0000717
DOID:1037	lymphoblastic leukemia	359	1.980895	0.0109087	0.0000717
DOID:10534	stomach cancer	231	1.962774	0.0115542	0.0000717
DOID:16	integumentary system disease	288	1.961439	0.0112197	0.0000717
DOID:854	collagen disease	159	1.951838	0.0120116	0.0000717
DOID:0050338	primary bacterial infectious disease	165	1.946575	0.0119726	0.0000717
DOID:2723	dermatitis	123	1.942831	0.0123286	0.0000717
DOID:9119	acute myeloid leukemia	93	1.940028	0.0378464	0.0001846
DOID:201	connective tissue cancer	338	1.931140	0.0109980	0.0000717
DOID:1575	rheumatic disease	147	1.923856	0.0121345	0.0000717
DOID:418	systemic scleroderma	147	1.923856	0.0121345	0.0000717
DOID:419	scleroderma	147	1.923856	0.0121345	0.0000717
DOID:5041	esophageal cancer	127	1.918541	0.0123009	0.0000717
DOID:3393	coronary artery disease	268	1.902290	0.0113295	0.0000717
DOID:1520	colon carcinoma	149	1.890664	0.0121177	0.0000717
DOID:409	liver disease	500	1.888508	0.0104810	0.0000717
DOID:526	Human immunodeficiency virus infectious disease	132	1.886409	0.0122519	0.0000717
DOID:170	endocrine gland cancer	443	1.883490	0.0106500	0.0000717
DOID:5844	myocardial infarction	220	1.873768	0.0116060	0.0000717
DOID:10283	prostate cancer	364	1.863541	0.0109001	0.0000717
DOID:1793	pancreatic cancer	276	1.859825	0.0112846	0.0000717
DOID:74	hematopoietic system disease	366	1.854196	0.0108872	0.0000717
DOID:0060100	musculoskeletal system cancer	395	1.852221	0.0107932	0.0000717
DOID:10591	pre-eclampsia	217	1.845411	0.0116364	0.0000717
DOID:5517	stomach carcinoma	133	1.835183	0.0488892	0.0002260
DOID:5683	hereditary breast ovarian cancer	200	1.828842	0.0117111	0.0000717
DOID:688	embryonal cancer	316	1.821178	0.0111069	0.0000717
DOID:3213	demyelinating disease	144	1.820715	0.0364894	0.0001803
DOID:2377	multiple sclerosis	138	1.819929	0.0366201	0.0001803
DOID:9352	type 2 diabetes mellitus	166	1.819645	0.0239338	0.0001260
DOID:2237	hepatitis	345	1.817577	0.0109721	0.0000717
DOID:3856	male reproductive organ cancer	372	1.814937	0.0108669	0.0000717
DOID:219	colon cancer	252	1.812164	0.0114349	0.0000717
DOID:2994	germ cell cancer	343	1.803332	0.0109889	0.0000717
DOID:4766	embryoma	298	1.801106	0.0111856	0.0000717
DOID:9256	colorectal cancer	256	1.800043	0.0113965	0.0000717
DOID:5672	large intestine cancer	257	1.790947	0.0113963	0.0000717
DOID:3996	urinary system cancer	426	1.790153	0.0106907	0.0000717
DOID:18	urinary system disease	387	1.788396	0.0108226	0.0000717
DOID:557	kidney disease	374	1.782717	0.0108602	0.0000717
DOID:4451	renal carcinoma	328	1.781683	0.0110522	0.0000717
DOID:3905	lung carcinoma	441	1.762810	0.0106577	0.0000717
DOID:114	heart disease	420	1.752559	0.0107121	0.0000717
DOID:4905	pancreatic carcinoma	206	1.751490	0.0233807	0.0001243
DOID:1492	eye and adnexa disease	441	1.748146	0.0106577	0.0000717
DOID:10155	intestinal cancer	268	1.747589	0.0113295	0.0000717
DOID:263	kidney cancer	375	1.745672	0.0108610	0.0000717
DOID:3908	non-small cell lung carcinoma	370	1.729466	0.0108690	0.0000717
DOID:120	female reproductive organ cancer	393	1.729094	0.0107987	0.0000717
DOID:184	bone cancer	224	1.727615	0.0231596	0.0001243
DOID:0050155	sensory system disease	489	1.726523	0.0105067	0.0000717
DOID:5614	eye disease	432	1.720764	0.0106620	0.0000717
DOID:1612	breast cancer	451	1.703644	0.0106239	0.0000717
DOID:5093	thoracic cancer	451	1.703644	0.0106239	0.0000717
DOID:15	reproductive system disease	281	1.677028	0.0337858	0.0001695
DOID:0050736	autosomal dominant disease	360	1.669221	0.0109122	0.0000717
DOID:10763	hypertension	482	1.559100	0.0316265	0.0001601

Enriched terms for module #00B9E3 (MTcor = -0.93)
ID	Description	setSize	NES	p.adjust	qvalues
DOID:2234	focal epilepsy	57	2.205412	0.0252781	0.000262
DOID:1826	epilepsy syndrome	191	2.070965	0.0109172	0.000262
DOID:0060041	autism spectrum disorder	166	1.800904	0.0334385	0.000262
DOID:12849	autistic disorder	166	1.800904	0.0334385	0.000262
DOID:0060040	pervasive developmental disorder	175	1.780626	0.0332072	0.000262

Enriched terms for module #84AD00 (MTcor = -0.93)
ID	Description	setSize	NES	p.adjust	qvalues
DOID:1826	epilepsy syndrome	191	2.01758	0.0148789	0.000146

Disease Gene Network

print_results(enrichment_DGN)